Research

This page has tables of our research publications broken down by category.

Journal Papers

Year Title Author Journal Link
2024 A compositional account of motifs, mechanisms, and dynamics in biochemical regulatory networks R. Aduddell, J. Fairbanks, A. Kumar, P.S. Ocal, E. Patterson, B.T. Shapiro Compositionality DOI
2024 Compositional Algorithms on Compositional Data: Deciding Sheaves on Presheaves E. Althaus, B. Bumpus, J. Fairbanks, D. Rosiak Fundamenta Informaticae DOI
2024 The Diagrammatic Presentation of Equations in Categories K. Arlin, J. Fairbanks, T. Hosgood, E. Patterson Journal of Pure and Applied Algebra DOI
2024 Towards a Unified Theory of Time-varying Data B. Bumpus, J. Fairbanks, M. Karvonen, W. Leal, F. Simard Proc. of the Royal Society Phil. Trans. DOI
2024 A Compositional Framework for First-Order Optimization T. Hanks, M Klawonn, M Hale, E Patterson, JP Fairbanks arxiv DOI
2023 Computational Category-Theoretic Rewriting K. Brown, E. Patterson, T. Hanks, J. Fairbanks J. Logical and Algebraic Methods in Programming DOI
2023 Decapodes: A Diagrammatic Tool for Representing, Composing, and Computing Spatialized Partial Differential Equations L. Morris, A. Baas, J. Arias, M. Gaitlin, E. Patterson, J. Fairbanks Journal of Computational Science DOI
2023 The application of applied category theory to quantify mission success R. Garrett, J. Fairbanks, M. Loper, J. Moreland SIMULATION 99 (2) 201-220 DOI
2022 Categorical Data Structures for Technical Computing E. J. Patterson, O. Lynch, J. P. Fairbanks Compositionality DOI
2022 A Diagrammatic View of Differential Equations in Physics E. Patterson, A. Baas, T. Hosgood, J. P. Fairbanks Mathematics in Engineering DOI
2022 An Algebraic Framework for Structured Epidemic Modeling S. Libkind, A. Baas, M. Halter, E. Patterson, and J. P. Fairbanks Proc. of the Royal Society Phil. Trans. DOI
2021 Category-theoretic formulation of the model-based systems architecting cognitive-computational Cycle Y. Mordecai, J. P. Fairbanks, E.F. Crawley MDPI Applied Sciences 11 (4), 1945 DOI
2017 Spectral Partitioning with Blends of Eigenvectors J. P. Fairbanks, D. A. Bader, G. D. Sanders Journal of Complex Networks DOI
2015 Behavioral Clusters in Dynamic Graphs J. P. Fairbanks, R. Kannan, H. Park, D. A. Bader Parallel Computing Special Issue of Scientific Graph Analysis DOI
2011 A Ramsey Theorem for Indecomposable Matchings J. P. Fairbanks Electronic Journal of Combinatorics, Vol 18(1) DOI
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Conference Papers

Year Title Author Venue Link
2024 Modeling Model Predictive Control: A Category Theoretic Framework for Multistage Control Problems Tyler Hanks, Baike She, Matthew Hale, Evan Patterson, Matthew Klawonn, James Fairbanks American Control Conference DOI
2024 Generalized Gradient Descent is a Hypergraph Functor T Hanks, M. Klawonn, J. Fairbanks Applied Category Theory DOI
2024 How Nice is this Functor? Two Squares and Some Homology go a Long Way B. Bumpus, D. Rosiak, C. Puca, F. Genovese, J. Fairbanks Applied Category Theory DOI
2024 Short Note on Cohomology, Sheafification and Lavish Presheaves B. Bumpus, D. Rosiak, M. Cappucci, J. Fairbanks Applied Category Theory DOI
2024 GATlab: Modeling and Programming with Generalized Algebraic Theories O Lynch, K Brown, JP Fairbanks, and E Patterson. https://arxiv.org/abs/2404.04837 DOI
2023 A Categorical Representation Language and Computational System for Knowledge-Based Planning A. Aguinaldo, E. Patterson, J. Fairbanks and J. Ruiz AAAI Fall Symposium on Unifying Representations for Robot Application Development DOI
2023 Characterizing Compositionality of LQR from the Categorical Perspective Baike She, Tyler Hanks, James Fairbanks, Matthew Hale IEEE Conf. Decision and Control DOI
2022 Compositional Exploration of Combinatorial Scientific Models K. Brown, T. Hanks, J. P. Fairbanks Applied Category Theory DOI
2022 Computational Category-Theoretic Rewriting K. Brown, E. Patterson, T. Hanks, J. P. Fairbanks International Conference on Graph Transformation (Best Paper Award) DOI
2021 Operadic Modeling of Dynamical Systems: Mathematics and Computation S. Libkind, A. Baas, E. J. Patterson, J. P. Fairbanks Applied category Theory (Proceedings) DOI
2020 SemanticModels.jl: A Julia Package for Scientific Model Augmentation M. Halter, S. Raparti, K. Cao, C. Herlihy, J. P. Fairbanks Proceedings of the JuliaCon Conferences DOI
2019 A Compositional Framework for Scientific Model Augmentation M. Halter, C. Herlihy, J. P. Fairbanks Applied Category Theory DOI
2019 Constructing Knowledge Graphs from Scientific Texts K. Cao, J. P. Fairbanks KDD workshop on Machine Learning in Graphs DOI
2019 Semantic Program Analysis for Scientific Model Augmentation J. P. Fairbanks, C. Herlihy, K. Cao, S. Reparthi Modeling the World’s Systems DOI
2018 Credibility Assessment in the News: Do we need to read? N. Fitch, N. Knauf, J. P. Fairbanks, E. Briscoe ACM WSDM MIS2 DOI
2018 Performance Effects of Backing Data Stores in Community Detection Algorithms R. Varkey Thankachan, B. P. Swenson, J. P. Fairbanks IEEE High Performance Extreme Computing DOI
2018 Digital Witness: Remote Methods for Volunteering Digital Evidence on Mobile Devices N. Campbell, T. Goodyear, W. Messer, E. Stuart, J. P. Fairbanks IEEE Technologies for Homeland Security DOI
2017 Integrating Productivity-Oriented Programming Languages with High-Performance Data Structures R. Varkey Thankachan, E. Hein, B. P. Swenson, J. P. Fairbanks IEEE High Performance Extreme Computing DOI
2017 Deriving Streaming Graph Algorithms from Static Definitions J. P. Fairbanks, D. M. Ediger IEEE International Parallel and Distributed Processing Graph Algorithms Building Blocks DOI
2017 Deriving Streaming Graph Algorithms from Static Definitions. D. M. Ediger and J. P. Fairbanks IEEE Parallel and Distributed Processing - Graph Algorithm Building Blocks DOI
2017 Graph Ranking Guarantees for Numerical Approximations to Katz Centrality E. Nathan, G. Sanders, J. P. Fairbanks, V. Henson and D. Bader International Conference On Computational Science DOI
2017 Ranking in Dynamic Graphs Using Exponential Centrality E. Nathan, J. P. Fairbanks, D. A. Bader International Conference on Complex Networks and their Applications DOI
2017 Graph Partitioning with Spectral Blends J. P. Fairbanks, D. A. Bader, and G. D. Sanders Oxford Journal of Complex Networks DOI
2016 Novel Stopping Criteria for Spectral Partitioning J. P. Fairbanks, A. Zakrzewska, D.A. Bader SIAM Network Science DOI
2013 A Statistical Framework for Analyzing Streaming Graphs J. P. Fairbanks, D. Ediger, R. McColl, D.A. Bader, E. Gilbert IEEE/ACM ASONAM DOI
  A local measure of community change in dynamic graphs. A. Zakrzewska, E. Nathan, J. P. Fairbanks, D. A. Bader IEEE/ACM ASONAM DOI
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Conference Talks

Year Title Author Venue Link
2022 Diagrammatic differential equations: Formal categorical framework and applications to multiphysics simulation, E. Patterson, T. Hosgood (speaker), A. Baas, J. Fairbanks Applied Category Theory 2022 DOI
2022 Individual.jl: Rewriting individual-based models for epidemiology using graph rewriting S. Wu (speaker), K. Browm, and J. Fairbanks Applied Category Theory 2022 DOI
2022 Typed and stratified models with slice categories S. Libkind (speaker), E. Patterson, A. Baas, M. Halter, J. Fairbanks Applied Category Theory 2022 DOI
2021 AlgebraicDynamics: Compositional dynamical systems S. Libkind, J. P. Fairbanks JuliaCon, Online DOI
2021 Shaped Data with Acsets O. Lynch, E. J. Patterson, J. P. Fairbanks JuliaCon, Online DOI
2021 Accelerating Automatic Target Recognition Performance Evaluation with a Relational Database M. Jackson, M. Halter, T. Goodyear, B. O’Donnell, and J. Fairbanks Tri-Service Radar Symposium DOI
2019 Complex Systems Analysis of Hybrid Warfare M. Nadolski and J. P. Fairbanks Conference on Systems Engineering Research DOI
2019 SemanticModels.jl: Not Just Another Modeling Framework J. P. Fairbanks and C. R. Herlihy JuliaCon, Baltimore, MD DOI
2018 The JuliaGraphs Ecosystem: Move Fast and Don’t Break Things J. P. Fairbanks JuliaCon, London, UK DOI
2017 Assessing Credibility in Global Media Networks J. P. Fairbanks Human Language Technologies DOI
2017 LightGraphs: Our Network, Our Story S. Bromberger, J. P. Fairbanks JuliaCon, Berkeley, CA DOI
2017 Using Big Data to Predict and Analyze Cooperation and Conflict T. Frederick, C. Herlihy, J. P. Fairbanks The Conflict Conference at UT-Austin DOI
  Graph Interfaces: Bespoke Graphs for Every Occasion M. Besanon, J. P. Fairbanks JuliaCon, London, UK DOI
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Preprints

Year Title
2024 Towards a Compositional Framework for Convex Analysis
Richard Samuelson and Dario Stein
2023 A Compositional Framework for Convex Model Predictive Control
Tyler Hanks, Baike She, Matthew Hale, Evan Patterson, Matthew Klawonn, and James Fairbanks